WO2010135514A2 - Sondes et amorces optimisées et leurs procédés d'utilisation pour la détection, le criblage, la quantification, l'isolement et le séquençage de cytomégalovirus et de virus epstein-barr - Google Patents

Sondes et amorces optimisées et leurs procédés d'utilisation pour la détection, le criblage, la quantification, l'isolement et le séquençage de cytomégalovirus et de virus epstein-barr Download PDF

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Publication number
WO2010135514A2
WO2010135514A2 PCT/US2010/035548 US2010035548W WO2010135514A2 WO 2010135514 A2 WO2010135514 A2 WO 2010135514A2 US 2010035548 W US2010035548 W US 2010035548W WO 2010135514 A2 WO2010135514 A2 WO 2010135514A2
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WO
WIPO (PCT)
Prior art keywords
seq
cmv
nos
group
ebv
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Application number
PCT/US2010/035548
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English (en)
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WO2010135514A3 (fr
Inventor
Damien Slater
James R. Hully
David Dolinger
Alice A. Jacobs
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Intelligent Medical Devices, Inc.
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Publication date
Application filed by Intelligent Medical Devices, Inc. filed Critical Intelligent Medical Devices, Inc.
Priority to CA2799995A priority Critical patent/CA2799995A1/fr
Priority to EP10778374A priority patent/EP2432793A4/fr
Publication of WO2010135514A2 publication Critical patent/WO2010135514A2/fr
Publication of WO2010135514A3 publication Critical patent/WO2010135514A3/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • C12Q1/705—Specific hybridization probes for herpetoviridae, e.g. herpes simplex, varicella zoster

Definitions

  • CMV and EBV target different tissue types in the host and, thus, have different clinical manifestations from one another.
  • CMV has a broad tissue tropism and is usually associated with retinitis, pneumonitis, encephalitis, hepatitis, and gastrointestinal disease.
  • CMV infection can cause blindness, hearing loss, and other neurological disorders.
  • EBV in contrast, is typically associated with lymphoproliferau've disorders and neoplasia, though it has also been implicated in cases of myocarditis, encephalitis, pneumonia, mesenteric adenitis, hepatitis, EBV mononucleosis, nasopharyngeal carcinoma and pancreatitis.
  • Acute EBV infection may often lead to a transient depression in the cell-mediated immune response (anergy), which affects an individual's ability to respond to other viral and intracellular bacterial pathogens.
  • the present invention is directed to a method for detecting and/or screening and/or quantitating EBV in a sample, comprising (1 ) at least one forward and reverse primer set selected from the group consisting of Groups 1 -71 and 148- 152 of Table 2 to a sample; (2) conducting an amplification process; and (3) detecting the generation of an amplified product, wherein the generation of an amplified product indicates the presence of EBV in the sample.
  • the present invention is directed to a method for detecting and/or screening and/or quantitating CMV and EBV in a sample simultaneously, comprising (1 ) contacting at least one multiplex set of a forward and reverse primer set listed in Table 2 to a sample; (2) conducting an amplification process; and (3) detecting the generation of an amplified product, wherein the generation of an amplified product indicates the presence of CMV and EBV in the sample.
  • Step (3) is performed using a combination of differently labeled multiplex CMV and EBV probes, or multiplex CMV and EBV probes labeled with the same detectable label.
  • the primer set and combination of probes is selected from the group consisting of Groups 1-152 of Table 2.
  • the present invention is directed to a kit for detecting and/or screening and/or quantitating CMV and/or EBV DNA, comprising: a) at least one forward primer comprising the sequence selected from the group consisting of: SEQ ID NOS: 1-36, 176, ISO, 182, 183, 186 and 191 ; b) at least one reverse primer comprising the sequence selected from the group consisting of: SEQ ID NOS: 109-170, 172, 178, 181, 185, 188 and 190; and c) one or more probes comprising a sequence selected from the group consisting of: SEQ IDNOS: 37-108, 171, 177, 179, 184, 187 and 189.
  • the present invention is directed to a method for diagnosing a CMV and/or EBV-associated condition, syndrome or disease, comprising: a) contacting a denatured target sequence from a sample with at least one probe selected from the group consisting of: SEQ ID NOS: 37-108, 171, 177, 179, 184, 187 and 189 for hybridization to occur, wherein the hybridization indicates the presence of CMV and/or EBV in the sample.
  • the present invention also provides multiplex panels that can be utilized for screening at least three important disease categories.
  • One of the panels includes screening individuals for CMV in combination with any of the following organisms for 'TORCH * ' infections: Toxoplasma gondii; Other, including hepatitis B virus, HIV, syphilis, varicella zoster virus, parvovirus B 19; Rubella; CMV; and Herpes simplex virus.
  • Primers and probes of the invention are sequences that anneal to a viral genomic or viral genomie derived sequence, e.g., CMV and EBV (the "target")-
  • the target sequence can be, for example, a viral genome or a subset, "region", of a viral genome.
  • the entire genomie sequence can be "scanned” for optimized primers and probes useful for detecting viral strains.
  • particular regions of the viral genome can be scanned, e.g.. regions that are documented in the literature as being useful for detecting multiple strains, regions that are conserved, or regions where sufficient information is available in, for example, a public database, with respect to viral strains.
  • the set of primers and probes are optimized for hybridizing to a plurality of viral strains by employing scoring and/or ranking steps that provide a positive or negative preference or "weight" to certain nucleotides in a target nucleic acid strain sequence. For example, if a consensus sequence is used to generate the full set of primers and probes, then a particular primer sequence is scored for its ability to anneal to the corresponding sequence of every known native strain sequence. Even if a probe were originally generated based on a consensus, therefore, the validation of the probe is in its ability to specifically anneal and detect every, or a large majority of, viral strain sequences.
  • Tm refers to the temperature at which a population of double-stranded nucleic acid molecules becomes half-dissociated into single strands.
  • the resultant scores represent steps in determining nucleotide or whole target nucleic acid sequence preference, while tailoring the primer and/or probe sequences so that they hybridize to a plurality of target nucleic acid strains.
  • the methods of determining the primers and probes also can comprise the step of allowing for one or more nucleotide changes when determining identity between the candidate primer and probe sequences and the target nucleic acid strain sequences, or their complements.
  • the methods of determining the primers and probes comprise the steps of comparing the candidate primer and probe nucleic acid sequences to "exclusion nucleic acid sequences" and then rejecting those candidate nucleic acid sequences that share identity with the exclusion nucleic acid sequences
  • the methods of the invention comprise the steps of comparing the candidate primer and probe nucleic acid sequences to "inclusion nucleic acid sequences” and then rejecting those candidate nucleic acid sequences that do not share identity with the inclusion nucleic acid sequences.
  • a diagnostic kit is provided by the present invention that comprises one or more of the oligonucleotides described herein, which are useful for detecting CMV and/or EBV infection in an individual and/or from a sample.
  • An individual can be a human male, human female, human adult, human child, or human fetus.
  • An individual can also be any mammal, reptile, avian, fish, or amphibian.
  • an individual can be a mouse, rat, sheep, dog, simian, horse, cattle, chicken, porcine, lamb, bird or fish.
  • a sample includes any item, surface, material, clothing, or environment, for example, sewage or water treatment plants, in which it may be desirable to test for the presence of CMV and/or EBV strains.
  • the present invention includes testing door handles, faucets, table surfaces, elevator buttons, chairs, toilet seats, sinks, kitchen surfaces, children's cribs, bed linen, pillows, keyboards, and so on, for the presence of CMV and/or EBV strains.
  • each oligonucleotide is located at a unique position on an array at least 2, at least 3, at least 4, at least 5, at least 6, or at least 10 times.
  • PCR-based methods are used to detect gene expression. These methods include reverse-transcriptaac-mcdiated polymerase chain reaction (RT-PCR) including real-time and endpoint quantitative reverse-transcriptasc- mediated polymerase chain reaction (Q-RTPCR). These methods are well known in the art For example, methods of quantitative PCR can be carried out using kits and methods that are commercially available from, for example, Applied BioSystems and Stratagene*.
  • RT-PCR reverse-transcriptaac-mcdiated polymerase chain reaction
  • Q-RTPCR real-time and endpoint quantitative reverse-transcriptasc- mediated polymerase chain reaction
  • the latter category of methods includes intercalation of dyes, such as, for example, ethidium bromide, into double-stranded nucleic acids, differential absorbance properties of double and single stranded nucleic acids, binding of proteins that preferentially bind double-stranded nucleic acids, and the like.
  • dyes such as, for example, ethidium bromide
  • Sequence #2 would, therefore, be the best choice if all the three bases with a score of 0.9 represented the same 9 target nucleic acid strain sequences, (iii) Overall Conservation Score of the Primer and Probe Set ••- Percent Identity [0090] The same method described in (ii) when applied to the complete primer set and probe set will generate the percent identity for the set (see A above). For example, using the same sequences illustrated above, if Sequences #1 and #2 are primers and Sequence #3 is a probe, then the percent identity for the target can be calculated from how many of the target nucleic acid strain sequences arc identified with perfect complimentarity by all three primer/probe sequences.
  • the total number of aligned sequences is considered under a coverage score.
  • a value is assigned to each position based on how many times mat position has been reported or sequenccd.
  • coverage can be defined as how representative the sequences are of the known strains, subtypes etc., or their relevance to a certain diseases. For example, the target nucleic acid strain sequences for a particular gene may be very well conserved and show complete coverage but certain strains are not represented in those sequences.
  • Candidate target strain sequences published in patents are searched electronically and annotated such that patented regions are excluded. Alternatively, candidate sequences are checked against a patented sequence database.
  • the methods of the present invention include analysts of nucleic acid secondary structure. This includes the structures of the primers and/or probes, as well as their intended target strain sequences.
  • the methods and software of the invention predict the optimal temperatures for annealing, but assumes that the target (e.g., RNA or DNA) does not have any significant secondary structure.
  • the target e.g., RNA or DNA
  • the first stage is the creation of a complimentary strand of DNA (cDNA) using a specific primer. This is usually performod at temperatures where the RNA template can have significant secondary structure thereby preventing the annealing of the primer.
  • a double stranded DNA target for example, an amplicon after PCR
  • the binding of the probe is dependent on there being no major secondary structure in the amplicon.
  • the methods and software of the invention may also analyze any nucleic acid sequence to determine its suitability in a nucleic acid amplification-based assay. For example, it can accept a competitor's primer set and determine the following information: (1) How it compares to the primers of the invention ⁇ e.g.. overall rank, PCR and conservation ranking, etc.); (2) How it aligns to the exclude libraries (e.g., assessing cross- hybridization) - also used to compare primer and probe sets to newly published sequences; and (3) If the sequence has been previously published. This step requires keeping a database of sequences published in scientific journals, posters, and other presentations.

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Zoology (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Virology (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention concerne des amorces et des sondes utiles pour la détection, le criblage, la quantification, l'isolement et le séquençage de souches virales CMV et EBV, et des procédés d'utilisation des amorces et sondes décrites.
PCT/US2010/035548 2009-05-22 2010-05-20 Sondes et amorces optimisées et leurs procédés d'utilisation pour la détection, le criblage, la quantification, l'isolement et le séquençage de cytomégalovirus et de virus epstein-barr WO2010135514A2 (fr)

Priority Applications (2)

Application Number Priority Date Filing Date Title
CA2799995A CA2799995A1 (fr) 2009-05-22 2010-05-20 Sondes et amorces optimisees et leurs procedes d'utilisation pour la detection, le criblage, la quantification, l'isolement et le sequencage de cytomegalovirus et de virus epstein-barr
EP10778374A EP2432793A4 (fr) 2009-05-22 2010-05-20 Sondes et amorces optimisées et leurs procédés d'utilisation pour la détection, le criblage, la quantification, l'isolement et le séquençage de cytomégalovirus et de virus epstein-barr

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US18067109P 2009-05-22 2009-05-22
US61/180,671 2009-05-22

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WO2010135514A2 true WO2010135514A2 (fr) 2010-11-25
WO2010135514A3 WO2010135514A3 (fr) 2011-01-27

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US (1) US20100297612A1 (fr)
EP (2) EP2631240A1 (fr)
CA (1) CA2799995A1 (fr)
WO (1) WO2010135514A2 (fr)

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US10265009B2 (en) 2014-10-21 2019-04-23 uBiome, Inc. Method and system for microbiome-derived diagnostics and therapeutics for conditions associated with microbiome taxonomic features
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US10357157B2 (en) 2014-10-21 2019-07-23 uBiome, Inc. Method and system for microbiome-derived characterization, diagnostics and therapeutics for conditions associated with functional features
US10395777B2 (en) 2014-10-21 2019-08-27 uBiome, Inc. Method and system for characterizing microorganism-associated sleep-related conditions
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Also Published As

Publication number Publication date
EP2432793A4 (fr) 2012-11-28
WO2010135514A3 (fr) 2011-01-27
US20100297612A1 (en) 2010-11-25
CA2799995A1 (fr) 2010-11-25
EP2631240A1 (fr) 2013-08-28
EP2432793A2 (fr) 2012-03-28

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